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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggttcgaaacatccttgcaacacttaacagaattttttttgaagtagtgttctgtggttttaattctagttttgtgcaggaattgacgtgctttgtgctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG

Basic information

species Physcomitrella patens
transcript PP1S101_184V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_184V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA07G29630.1 (Glycine max), 3'ss of exon 4
gtttggttcgaaacatccttgcaacacttaacagaattttttt-tgaagtagtgttctgtggttttaattcta-gttttgtgcaggaattgacgtgctttgtgctcgttc-cagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG
        |   |  | |||| | || |   ||     |  || |||| || ||  | || | |  | |  || ||    | ||  | ||||   ||||    |  |||  ||||| |||||  |  || | ||| | ||||||||  | || ||  | ||||| ||||||||||||||| | ||||||||||| ||||||
--------catcattttcttg-agcaatcctcatggcatgattatgaaata-tgcac-gtcgatgcattgttatgtaaattacataatttga---gcttaacccatgtttgcagGACTTGCCAGATTTGATTGCAATAAAGGATGCAAACTTTTCTGATGTGGATGCTGTATTCTGTTGTTTGCCTCATGGAACTACTCAG

upper sequence: PP1S101_184V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA20G01220.1 (Glycine max), 3'ss of exon 3
gtttggttcgaaacatccttgcaacacttaacagaattttttttgaagtagtgttctgtggttttaattcta-gttttgtgcaggaattga-cgtgctttgtgctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG
        |   |  | |||| | || |   ||     |  ||   | |  ||   ||| | |  | |  || ||    | ||  | |||| | |      || | |   ||||| |||||  |  || |  || | ||||||||  | || ||  | ||||| ||||||||||||||| | ||||||||||| ||||||
--------catcattttcttg-agcaatcctcatggcgtgattatgaattatgca-tgttgatgcactgttatgtaaattacataatttgaacttaacccatgtttg---cagGACTTGCCAGATTTGATTTCAATAAAGGATGCAAACTTTTCTGATGTGGATGCTGTATTCTGTTGTTTGCCTCATGGAACTACTCAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|162261824|gb|FC438348.1|FC438348
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|162265711|gb|FC443117.1|FC443117
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|100427283|gb|BY959068.1|BY959068
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|100365102|gb|BY966811.1|BY966811
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|18352338|gb|BJ184392.1|BJ184392
EST:     GAAAGGCAGGCCAGTCCTTANCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCA
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCA
EST: gi|100383898|gb|BY987155.1|BY987155
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCACAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|162179978|gb|FC356049.1|FC356049
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|162168515|gb|FC344452.1|FC344452
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|100431865|gb|BY978545.1|BY978545
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|67508394|gb|BJ941261.1|BJ941261
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|100379495|gb|BY949797.1|BY949797
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|162234961|gb|FC411748.1|FC411748
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|100397985|gb|BY954031.1|BY954031
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|100398471|gb|BY972624.1|BY972624
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|100445108|gb|BY964407.1|BY964407
EST:     GAAAGGCAGGGCAGTCTTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCCGATTTCTCGCAGGTGGA
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCC-GATTTCTCGCAGGTGGA
EST: gi|100449342|gb|CJ973641.1|CJ973641
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC
EST: gi|100389059|gb|BY952263.1|BY952263
EST:     GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAG                         GATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCANGTGGAC
genomic: GAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 24 (upstream exon), 31 (downstream exon)
Score: 5

CCTGCTAGCGACACACCCAGTCTTTAAAGTGACAATGATGACAGCCGATCGAAAGGCAGGCCAGTCCTTAGCATCCGTCTTCCCTCATCTGGCTACACAGgtttggttcg ... ctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggttttaattctagttttgtgcaggaattgacgtgctttgtgctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG
                            aattgac  putative branch site (score: 5)
                                             ctcgttcc  putative PPT
     ttttaattctagtttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggttcgaaacatccttgcaacacttaacagaattttttttgaagtagtgttctgtggttttaattctagttttgtgcaggaattgacgtgctttgtgctcgttccagGATTTGCCGAACATGGTCGCAGTCAAGGATGCCGATTTCTCGCAGGTGGACGCTGTATTCTGTTGTCTTCCTCATGGAACAACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA